Anki (or any other SRS) doesn't have to be about learning words out of context. I've learned a lot with Anki plus sentences off of Tatoeba, which has a large amount of sentences translated into many languages. And I did that while being familiar with the basics of Krashen's ideas. I think there's no contradiction. Learning words and not forgetting them helps me to focus on getting a lot of input on my target language, without the drudge of (re-)looking up the dictionary for every other word.

http://tatoeba.org/eng/

By the way, (for the benefit of other people reading this) the website you link to has many other interesting articles about language learning vs. acquisition.